Contacts of the helix formed by residues 21 - 52 (chain B) in PDB entry 3D0G
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 21 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B THR* 1.3 86.2 + - - +
22B GLU* 1.3 65.6 + - - +
23B GLU 2.9 1.1 - - - +
24B LEU* 3.0 8.8 + - + +
25B ALA* 3.0 24.1 + - + +
83B TYR* 4.9 8.3 - - + -
84B PRO* 4.4 24.2 - - + +
87B GLU* 2.9 35.7 + - - +
88B ILE* 5.0 7.6 - - + -
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Residues in contact with GLU 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B THR* 3.9 3.5 + - - +
21B THR* 1.3 78.5 - - - +
23B GLU* 1.3 62.3 + - - +
25B ALA* 3.6 7.6 + - - +
26B LYS* 3.1 47.7 + - - +
88B ILE* 3.2 18.8 - - + +
89B GLN* 2.9 52.8 + - - +
90B ASN* 3.0 27.8 + - - +
93B VAL* 4.4 3.5 - - + +
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Residues in contact with GLU 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B SER* 4.2 20.3 + - - +
20B THR* 3.3 30.3 + - - +
21B THR 2.9 0.4 - - - +
22B GLU* 1.3 76.6 - - - +
24B LEU* 1.3 63.0 + - - +
25B ALA 3.1 1.2 + - - -
26B LYS* 3.1 31.2 + - - +
27B THR* 3.7 8.9 + - - -
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Residues in contact with LEU 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B SER* 4.5 22.9 - - - +
20B THR 3.4 23.3 - - - +
21B THR* 3.0 9.1 + - + +
23B GLU* 1.3 78.6 - - + +
25B ALA* 1.3 60.2 + - - +
27B THR* 3.9 7.5 + - - -
28B PHE* 3.5 20.3 + - - +
83B TYR* 3.9 19.4 + - + +
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Residues in contact with ALA 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B THR* 3.0 15.5 + - + +
22B GLU* 3.6 9.6 - - + +
24B LEU* 1.3 75.1 - - - +
26B LYS* 1.3 65.9 + - - +
28B PHE* 3.2 5.4 + - - +
29B LEU* 3.0 35.6 + - + +
83B TYR* 4.0 21.7 - - + -
88B ILE* 4.5 16.8 - - + -
93B VAL* 5.7 5.2 - - + -
97B LEU* 4.8 5.2 - - + -
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Residues in contact with LYS 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B GLU* 3.1 39.5 + - - +
23B GLU* 3.1 19.5 + - - +
25B ALA* 1.3 76.2 - - - +
27B THR* 1.3 54.9 + - - +
29B LEU* 2.9 11.4 + - - +
30B GLU* 2.8 49.0 + - - +
90B ASN* 4.1 8.7 - - - -
93B VAL* 3.7 30.0 - - + +
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Residues in contact with THR 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B GLU 3.7 10.1 + - - -
24B LEU* 4.0 9.2 - - - -
25B ALA 3.4 0.2 - - - -
26B LYS* 1.3 76.2 - - - +
28B PHE* 1.3 57.0 + - - +
30B GLU* 3.4 16.5 + - + +
31B THR* 3.0 37.9 + - - +
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Residues in contact with PHE 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU 3.5 6.2 + - - +
25B ALA 3.2 9.6 + - - +
26B LYS 3.2 0.4 - - - -
27B THR* 1.3 78.7 - - - +
29B LEU* 1.3 63.2 + - + +
31B THR* 3.2 8.3 + - + -
32B PHE* 2.8 26.9 + - + +
76B GLN* 3.3 29.6 - - - -
79B LEU* 4.2 15.5 - - + -
80B ALA* 3.9 27.6 - - + -
83B TYR* 3.8 36.3 - + + +
97B LEU* 4.4 9.9 - - + -
100B LEU* 3.7 31.9 - - + -
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Residues in contact with LEU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ALA* 3.0 29.9 + - + +
26B LYS* 2.9 9.3 + - - +
28B PHE* 1.3 77.7 - - + +
30B GLU* 1.3 58.2 - - - +
32B PHE* 3.0 5.3 + - + +
33B ASN* 2.7 40.3 + - - +
93B VAL* 4.3 21.5 - - + +
96B GLN* 4.2 27.1 - - + +
97B LEU* 3.8 23.6 - - + +
100B LEU* 4.0 19.7 - - + -
391B LEU* 3.9 26.5 - - + -
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Residues in contact with GLU 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LYS* 2.8 34.6 + - - +
27B THR* 3.5 17.8 + - + +
29B LEU* 1.3 70.7 - - - +
31B THR* 1.3 62.9 + - - +
33B ASN* 3.3 10.1 + - - +
34B TYR* 3.1 44.5 + - + -
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Residues in contact with THR 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B THR* 3.0 19.1 + - - +
28B PHE* 3.5 11.2 - - + -
29B LEU 3.1 0.2 - - - -
30B GLU* 1.3 72.7 - - - +
32B PHE* 1.3 67.2 + - - +
34B TYR* 3.3 7.1 + - - +
35B GLU* 3.1 28.8 + - + +
76B GLN* 6.2 2.0 - - - +
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Residues in contact with PHE 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B PHE* 2.8 18.0 + - + +
29B LEU* 3.3 10.8 - - + +
31B THR* 1.3 74.1 - - - +
33B ASN* 1.3 66.7 + - - +
35B GLU* 3.6 1.5 - - - +
36B ALA* 2.6 57.1 + - + +
72B PHE* 3.9 20.1 - + - -
73B LEU* 4.0 17.9 - - + -
76B GLN* 3.7 31.6 + - + +
100B LEU* 3.6 35.7 - - + -
390B PHE* 4.1 5.4 - + - -
391B LEU* 3.6 41.5 - - + -
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Residues in contact with ASN 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU* 2.7 20.1 + - - +
30B GLU* 3.3 13.9 - - - +
32B PHE* 1.3 90.7 - - - +
34B TYR* 1.3 66.6 + - + +
36B ALA* 3.2 3.2 + - - +
37B GLN* 3.0 35.0 + - - +
96B GLN* 3.6 24.6 + - - +
389B PRO* 5.0 1.9 - - - +
390B PHE* 3.5 29.5 + - + +
391B LEU* 4.4 3.6 - - - +
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Residues in contact with TYR 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B GLU* 3.1 43.0 + - + +
31B THR* 4.1 5.2 - - - +
33B ASN* 1.3 82.3 - - + +
35B GLU* 1.3 62.2 + - - +
37B GLN* 3.8 16.5 + - - +
38B GLU* 3.4 25.6 + - - +
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Residues in contact with GLU 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B THR* 3.1 22.6 + - + +
32B PHE* 3.8 2.5 - - - +
34B TYR* 1.3 75.2 - - - +
36B ALA* 1.3 65.8 + - - +
38B GLU* 3.3 14.2 + - - +
39B LEU* 3.1 45.1 + - - +
72B PHE* 3.8 19.4 - - + -
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Residues in contact with ALA 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B PHE* 2.6 45.4 + - + +
33B ASN 3.2 4.2 + - - +
35B GLU* 1.3 71.5 - - - +
37B GLN* 1.3 54.3 + - - +
39B LEU 3.1 1.6 + - - -
40B SER* 2.7 39.0 + - - -
69B TRP* 3.3 29.0 - - + -
72B PHE* 3.7 5.4 - - + -
390B PHE* 3.9 9.4 - - + -
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Residues in contact with GLN 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ASN* 3.0 23.5 + - - +
34B TYR* 3.9 17.9 - - - +
35B GLU 3.2 0.2 - - - -
36B ALA* 1.3 75.0 - - - +
38B GLU* 1.3 59.0 + - - +
40B SER* 3.7 0.9 - - - -
41B TYR* 2.9 33.1 + - - +
353B LYS* 3.0 32.2 + - + +
390B PHE* 3.9 26.6 - - + +
393B ARG* 3.2 27.5 - - - +
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Residues in contact with GLU 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B TYR 3.4 17.2 + - - +
35B GLU* 3.3 18.8 + - - +
37B GLN* 1.3 76.5 - - - +
39B LEU* 1.3 64.8 + - + +
41B TYR* 4.0 3.8 - - - +
42B GLN* 3.3 32.4 + - - +
353B LYS* 3.1 34.8 + - - +
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Residues in contact with LEU 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B GLU* 3.1 26.6 + - - +
36B ALA 3.1 3.6 + - - +
38B GLU* 1.3 78.8 - - + +
40B SER* 1.3 57.4 + - - +
42B GLN* 3.3 20.1 + - - +
43B SER* 3.0 26.9 + - - -
65B ALA 4.9 1.6 - - - +
68B LYS* 3.7 35.4 - - + +
69B TRP* 3.5 22.5 - - + +
72B PHE* 3.4 41.5 - - + -
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Residues in contact with SER 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ALA 2.7 21.0 + - - -
37B GLN 3.9 2.2 - - - -
39B LEU* 1.3 70.4 - - - +
41B TYR* 1.3 62.9 + - - +
43B SER* 3.5 6.5 + - - -
44B SER* 2.8 31.0 + - - -
69B TRP* 3.7 31.5 + - - -
351B LEU 4.3 4.0 + - - -
390B PHE* 3.9 19.0 - - - -
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Residues in contact with TYR 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B GLN 2.9 17.2 + - - +
38B GLU* 4.0 4.9 - - - +
40B SER* 1.3 74.7 - - - +
42B GLN* 1.3 64.1 + - + +
44B SER* 2.9 2.9 + - - -
45B VAL* 2.9 54.1 + - + +
351B LEU* 3.4 22.8 + - + +
352B GLY* 3.5 26.0 - - - -
353B LYS* 4.0 27.1 - - + -
355B ASP* 2.7 31.0 + - + +
357B ARG* 4.5 1.6 + - - -
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Residues in contact with GLN 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B GLU* 3.3 18.1 + - - +
39B LEU* 3.5 26.8 - - - +
41B TYR* 1.3 82.0 - - + +
43B SER* 1.3 58.0 + - - +
45B VAL* 4.4 4.6 - - - +
46B ALA* 3.1 27.0 + - - +
65B ALA* 3.5 13.3 - - + +
68B LYS* 4.6 9.3 + - - +
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Residues in contact with SER 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU 3.0 13.7 + - - -
40B SER* 3.5 11.9 - - - -
41B TYR 3.1 0.2 - - - -
42B GLN* 1.3 76.6 - - - +
44B SER* 1.3 54.1 + - - +
46B ALA* 3.3 2.8 - - - +
47B SER* 2.7 34.9 + - - -
62B MET 5.0 2.3 - - - +
65B ALA* 3.8 14.5 - - - +
66B GLY* 3.9 13.2 - - - +
69B TRP* 4.1 25.6 - - - -
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Residues in contact with SER 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B SER* 2.8 17.8 + - - -
41B TYR 2.9 5.7 + - - -
43B SER* 1.3 73.9 - - - +
45B VAL* 1.3 59.2 + - - +
46B ALA 3.0 1.1 - - - -
47B SER* 2.9 7.8 + - - -
48B TRP* 2.6 36.0 + - - +
349B TRP* 3.8 7.7 - - - -
350B ASP 5.0 0.9 + - - -
351B LEU* 3.3 38.1 + - - -
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Residues in contact with VAL 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B TYR* 2.9 61.8 + - + +
42B GLN* 4.4 4.5 - - - +
44B SER* 1.3 74.0 - - - +
46B ALA* 1.3 65.4 + - - +
48B TRP* 3.8 2.1 - - - +
49B ASN* 3.2 34.0 + - - +
351B LEU* 3.6 14.8 - - + +
357B ARG* 4.9 8.7 - - - +
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Residues in contact with ALA 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B GLN 3.1 22.3 + - - +
43B SER 3.3 4.7 - - - +
44B SER 3.0 0.4 - - - -
45B VAL* 1.3 71.5 - - - +
47B SER* 1.3 68.7 + - - +
48B TRP 2.8 2.4 + - - -
49B ASN* 2.8 18.8 + - - +
50B TYR* 3.3 8.0 + - - +
58B ASN 5.4 0.5 - - - +
61B ASN* 4.0 13.9 - - + +
62B MET* 3.7 28.1 - - - +
65B ALA* 4.1 6.3 - - + -
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Residues in contact with SER 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B SER* 2.7 22.8 + - - -
44B SER* 2.9 7.1 + - - -
46B ALA* 1.3 72.7 - - - +
48B TRP* 1.3 59.1 + - - +
50B TYR* 3.5 3.3 + - - +
51B ASN* 2.4 36.4 + - - +
62B MET* 3.1 25.9 - - - +
349B TRP* 3.4 18.5 - - - -
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Residues in contact with TRP 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B SER 2.6 20.3 + - - +
45B VAL* 3.8 4.3 - - + +
46B ALA 2.8 1.6 + - - -
47B SER* 1.3 67.1 - - - +
49B ASN* 1.3 72.3 + - - +
50B TYR 3.0 4.5 - - - -
51B ASN* 2.8 23.4 + - - +
52B THR* 2.8 38.6 + - + +
330B ASN 3.3 21.6 + - - -
331B SER 4.3 0.2 - - - -
332B MET* 3.9 10.8 - - + -
349B TRP* 3.4 56.4 - + + -
351B LEU* 4.2 7.6 - - + -
357B ARG* 3.0 43.4 - - + +
358B ILE 3.8 18.4 - - - -
359B LEU* 3.7 23.6 - - + -
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Residues in contact with ASN 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B VAL* 3.2 26.7 + - - +
46B ALA* 2.8 10.6 + - - +
48B TRP* 1.3 90.6 + - - +
50B TYR* 1.3 55.8 + - - +
52B THR* 3.5 7.4 + - - -
53B ASN* 3.0 29.6 + - + +
58B ASN* 3.1 20.1 + - + +
357B ARG* 5.1 0.5 + - - -
----------------------------------------------------------
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Residues in contact with TYR 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ALA 3.3 4.0 + - - -
47B SER 3.5 7.6 - - - +
48B TRP 3.0 0.6 - - - -
49B ASN* 1.3 74.8 - - - +
51B ASN* 1.3 73.5 + - - +
52B THR 2.9 10.7 + - - -
53B ASN 3.0 22.6 + - - -
54B ILE* 3.4 40.9 + - + +
58B ASN* 4.2 6.4 - - - +
59B VAL* 3.6 47.3 - - + +
62B MET* 4.0 31.2 - - + -
343B VAL* 4.5 18.2 - - + +
----------------------------------------------------------
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Residues in contact with ASN 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B SER* 2.4 35.4 + - - +
48B TRP 2.8 11.7 + - - +
50B TYR* 1.3 83.8 - - - +
52B THR* 1.3 57.6 + - - +
53B ASN 3.7 0.2 - - - -
62B MET* 4.6 2.4 - - - +
342B ALA* 3.3 6.4 - - - +
343B VAL* 3.2 52.1 + - + +
349B TRP* 4.1 13.9 - - + -
359B LEU* 3.5 25.7 - - + +
----------------------------------------------------------
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Residues in contact with THR 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B TRP* 2.8 50.5 + - + +
49B ASN* 3.5 12.1 + - - -
51B ASN* 1.3 82.8 - - - +
53B ASN* 1.3 63.0 + - - +
332B MET* 3.7 34.6 - - + +
340B GLN* 3.7 18.5 + - - +
341B LYS 4.0 6.4 - - - +
342B ALA* 3.8 7.8 - - - +
359B LEU* 4.0 10.3 - - + -
----------------------------------------------------------
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il